Stretching alone is sometimes not enough to prevent injuries in the case where the muscles have developed knots. The best way to prevent these knots is a foam roller, a firm log 6 inches in diameter that can put pressure against them with the help of your body weight.
Here are some tips for using them:
1. Roll back and forth across the painful or stiff area for 60 seconds.
2. Spend extra time directly over the knot or trigger point itself.
3. Roll the injured area two to three times a day. For prevention of injuries, two to three times a week is recommended.
4. Avoid rolling over bony areas.
5. Always stretch the area following foam rolling.
Spend some time on google to find the following exercises:
IT band roll, quad roll, hamstring roll, calves roll
Here is a Runner's World article that has a few descriptions: